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failed upload of ProtProphet data

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failed upload of ProtProphet data tvaisar  2015-10-01 05:47
Status: Closed
 
Hi,

I am not sure what is wrong, but I tried to upload Comet search results from shotgun proteomics LCMS acquired on Thermo Fusion and the upload failed with the following in the log file (below).
I was able to upload Comet search results and shotgun proteomics from Fusion before.
I noticed that in reading the mzXML file it shows MS3: 0 and I am sure that is incorrect.
Any suggestions?

Thanks,

Tomas
 
01 Oct 2015 05:23:34,566 INFO : Starting to load ProteinProphet file /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.prot.xml

01 Oct 2015 05:23:34,587 INFO : Resolved referenced PepXML file to /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,588 INFO : Starting import from interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,595 INFO : Starting to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 DEBUG: 0.03 seconds to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 INFO : Starting to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,058 INFO : FASTA file "/data/dbase/Uniprot/uniprot.sptr.human.20150718" not imported, but another file, 'uniprot.sptr.human.20150718', has the same checksum

01 Oct 2015 05:23:35,062 DEBUG: 0.43 seconds to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,062 INFO : Starting to import peptide search results

01 Oct 2015 05:23:35,062 INFO : Importing MS/MS results is 0% complete

01 Oct 2015 05:23:35,063 INFO : Starting to parse /data/users/tvaisar/HDL/LRA/1509Shotgun/150909_LRAPEGJW01.mzXML to get scan counts

01 Oct 2015 05:23:38,125 INFO : Finished parsing to get scan counts. Total: 53396, MS1: 7724, MS2: 45672, MS3: 0, MS4:0

01 Oct 2015 05:23:38,144 ERROR: MS2 import failed

java.lang.ArrayIndexOutOfBoundsException

01 Oct 2015 05:23:38,154 ERROR: ProteinProphet load failed

java.lang.ArrayIndexOutOfBoundsException
 
 
Jon (LabKey DevOps) responded:  2015-10-01 11:39
Hi Tomas,

Any chance you have the full stack error? This will help us greatly.

You should be able to get the full log from the pipeline job by clicking on the option to view the full log link where you got this summarized log data.

Regards,

Jon
 
tvaisar responded:  2015-10-01 12:38
Jon,

This is the whole logfile info. (not much more) - any other log file would help?

01 Oct 2015 05:23:34,566 INFO : Starting to load ProteinProphet file /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.prot.xml

01 Oct 2015 05:23:34,587 INFO : Resolved referenced PepXML file to /data/users/tvaisar/HDL/LRA/1509Shotgun/interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,588 INFO : Starting import from interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,595 INFO : Starting to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 DEBUG: 0.03 seconds to clear out any previously imported data for interact-150909_LRAPEGJW01.pep.xml

01 Oct 2015 05:23:34,627 INFO : Starting to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,058 INFO : FASTA file "/data/dbase/Uniprot/uniprot.sptr.human.20150718" not imported, but another file, 'uniprot.sptr.human.20150718', has the same checksum

01 Oct 2015 05:23:35,062 DEBUG: 0.43 seconds to import FASTA file /data/dbase/Uniprot/uniprot.sptr.human.20150718

01 Oct 2015 05:23:35,062 INFO : Starting to import peptide search results

01 Oct 2015 05:23:35,062 INFO : Importing MS/MS results is 0% complete

01 Oct 2015 05:23:35,063 INFO : Starting to parse /data/users/tvaisar/HDL/LRA/1509Shotgun/150909_LRAPEGJW01.mzXML to get scan counts

01 Oct 2015 05:23:38,125 INFO : Finished parsing to get scan counts. Total: 53396, MS1: 7724, MS2: 45672, MS3: 0, MS4:0

01 Oct 2015 05:23:38,144 ERROR: MS2 import failed

java.lang.ArrayIndexOutOfBoundsException

01 Oct 2015 05:23:38,154 ERROR: ProteinProphet load failed

java.lang.ArrayIndexOutOfBoundsException
 
Jon (LabKey DevOps) responded:  2015-10-01 13:21
Hi Tomas,

Do you have access to the Labkey.log file? That should show the full stack.

Regards,

Jon
 
tvaisar responded:  2015-10-01 13:29
Jon,

not much more there. I actually found out that other user had the error couple days ago and did not tell me.
Attached is the last 200 lines from labkey.log file.

Tomas
 
Jon (LabKey DevOps) responded:  2015-10-01 15:33
Hi Tomas,

Thanks for providing the file. We're taking a look to see if we can gain any additional insight from the log section you provided.

In the meantime, can you let us know what version and build of LabKey you're running (you can get this from the Admin Console section under Modules) and database version as well?

Regards,

Jon
 
tvaisar responded:  2015-10-01 15:41
Thanks Jon,
It's Labkey 15.20, and PosgreSQL 9.4.4.

Tomas
 
tvaisar responded:  2015-10-03 08:08
Well, embarrassing to say, but the fix was simple - to restart tomcat.
Thanks for help.

Tomas
 
Jon (LabKey DevOps) responded:  2015-10-05 10:41
Hi Tomas,

Glad to know that it's working for you. We're still going to keep tabs on this issue on our end. The error itself unfortunately doesn't give enough to do a proper investigation, but if we see this re-occur with any of our other clients, we might be able to find a pattern or at least something that will give us a better clue as to what is going on then.

Regards,

Jon